Quick Guide to Multi-Protein Analysis

Multi-Protein Quantitation, Multi-Protein Identification, and Multi-Protein Preview Workflows

Figure 1: Multi-Protein workflow icons

The Multi-Protein workflows each have three separate tabs: Samples, Sequences, and Processing nodes. Project Creation steps differ between each workflow. Below outlines the process of Project Creation using the Multi-Protein Identification workflow. Additional details on each workflow can be found in the Byos User Manual.

Create a Workflow

Click to launch any of the above mentioned workflows. The below steps highlight creation using the Multi-Protein Identification workflow.

Figure 2: Multi-Protein Identification icon

Drag and drop the sample file(s) to be processed into the Samples tab, as shown in the figure below:

Figure 3: Drag and drop sample data files to be processed into the Samples tab

In the Sequences tab, specify the FASTA database:

Figure 4: Pointing to FASTA in Project Creation

Either manually enter the enzyme specificity and fixed modification based upon the alkylating reagent used, or simply import the search parameters created by the Multi-Protein Preview analysis

On the Processing tab of the workflow editor, right click on the Multi-Protein Identification node to display the context menu, select Load byparms:

Figure 5: Load Byparms in Processing nodes

Browse and select the parameter file created by Preview:

Figure 6: Open byparms

If desired, modify the suggested search parameters:

Figure 7: Manual modification of Digestion parameters

Browse to a Target output folder and enter a desired project name:

Figure 8: Select target folder

Click Create Project to begin analysis. Depending upon the size of the data and/or fasta databases used, your protein identification results should be available in a relatively short period of time.

From the open result, apply filters to the Protein view to focus on the highest ranked proteins:

Figure 9: Column Filter Editor for Proteins View